1
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Lyons PJ. Inactive metallopeptidase homologs: the secret lives of pseudopeptidases. Front Mol Biosci 2024; 11:1436917. [PMID: 39050735 PMCID: PMC11266112 DOI: 10.3389/fmolb.2024.1436917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. Other metallopeptidase families contain pseudopeptidases involved in protein synthesis at the ribosome and protein import into organelles, sometimes using their pseudo-active sites for these interactions. Although the functions of these pseudopeptidases have been challenging to study, ongoing work is teasing out the secret lives of these proteins.
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Affiliation(s)
- Peter J. Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, United States
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2
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Sun C, Cheng X, Xu J, Chen H, Tao J, Dong Y, Wei S, Chen R, Meng X, Ma Y, Tian H, Guo X, Bi S, Zhang C, Kang J, Zhang M, Lv H, Shang Z, Lv W, Zhang R, Jiang Y. A review of disease risk prediction methods and applications in the omics era. Proteomics 2024:e2300359. [PMID: 38522029 DOI: 10.1002/pmic.202300359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
Risk prediction and disease prevention are the innovative care challenges of the 21st century. Apart from freeing the individual from the pain of disease, it will lead to low medical costs for society. Until very recently, risk assessments have ushered in a new era with the emergence of omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and so on, which potentially advance the ability of biomarkers to aid prediction models. While risk prediction has achieved great success, there are still some challenges and limitations. We reviewed the general process of omics-based disease risk model construction and the applications in four typical diseases. Meanwhile, we highlighted the problems in current studies and explored the potential opportunities and challenges for future clinical practice.
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Affiliation(s)
- Chen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Xiangshu Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Jing Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Haiyan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junxian Tao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Yu Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Rui Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yingnan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
| | - Hongsheng Tian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xuying Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuo Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jingxuan Kang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- The EWAS Project, Harbin, China
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3
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Lütge A, Lu J, Hüllein J, Walther T, Sellner L, Wu B, Rosenquist R, Oakes CC, Dietrich S, Huber W, Zenz T. Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia. Haematologica 2023; 108:2664-2676. [PMID: 37226709 PMCID: PMC10614035 DOI: 10.3324/haematol.2022.281869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
Understanding the molecular and phenotypic heterogeneity of cancer is a prerequisite for effective treatment. For chronic lymphocytic leukemia (CLL), recurrent genetic driver events have been extensively cataloged, but this does not suffice to explain the disease's diverse course. Here, we performed RNA sequencing on 184 CLL patient samples. Unsupervised analysis revealed two major, orthogonal axes of gene expression variation: the first one represented the mutational status of the immunoglobulin heavy variable (IGHV) genes, and concomitantly, the three-group stratification of CLL by global DNA methylation. The second axis aligned with trisomy 12 status and affected chemokine, MAPK and mTOR signaling. We discovered non-additive effects (epistasis) of IGHV mutation status and trisomy 12 on multiple phenotypes, including the expression of 893 genes. Multiple types of epistasis were observed, including synergy, buffering, suppression and inversion, suggesting that molecular understanding of disease heterogeneity requires studying such genetic events not only individually but in combination. We detected strong differentially expressed gene signatures associated with major gene mutations and copy number aberrations including SF3B1, BRAF and TP53, as well as del(17)(p13), del(13)(q14) and del(11)(q22.3) beyond dosage effect. Our study reveals previously underappreciated gene expression signatures for the major molecular subtypes in CLL and the presence of epistasis between them.
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Affiliation(s)
- Almut Lütge
- Genome Biology Unit, EMBL, Heidelberg, Germany; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich
| | - Junyan Lu
- Genome Biology Unit, EMBL, Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg
| | | | - Tatjana Walther
- Molecular Therapy in Hematology and Oncology and Department of Translational Oncology, NCT and DKFZ, Heidelberg
| | - Leopold Sellner
- Molecular Therapy in Hematology and Oncology and Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany; Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Bian Wu
- Molecular Therapy in Hematology and Oncology and Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany; Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics, Karolinska University Hospital, Solna
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | | | - Thorsten Zenz
- Molecular Therapy in Hematology and Oncology and Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany; Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich.
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5
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Liang X, Meng Y, Li C, Liu L, Wang Y, Pu L, Hu L, Li Q, Zhai Z. Super-Enhancer–Associated nine-gene prognostic score model for prediction of survival in chronic lymphocytic leukemia patients. Front Genet 2022; 13:1001364. [PMID: 36186463 PMCID: PMC9521409 DOI: 10.3389/fgene.2022.1001364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a type of highly heterogeneous mature B-cell malignancy with various disease courses. Although a multitude of prognostic markers in CLL have been reported, insights into the role of super-enhancer (SE)–related risk indicators in the occurrence and development of CLL are still lacking. A super-enhancer (SE) is a cluster of enhancers involved in cell differentiation and tumorigenesis, and is one of the promising therapeutic targets for cancer therapy in recent years. In our study, the CLL-related super-enhancers in the training database were processed by LASSO-penalized Cox regression analysis to screen a nine-gene prognostic model including TCF7, VEGFA, MNT, GMIP, SLAMF1, TNFRSF25, GRWD1, SLC6AC, and LAG3. The SE-related risk score was further constructed and it was found that the predictive performance with overall survival and time-to-treatment (TTT) was satisfactory. Moreover, a high correlation was found between the risk score and already known prognostic markers of CLL. In the meantime, we noticed that the expressions of TCF7, GMIP, SLAMF1, TNFRSF25, and LAG3 in CLL were different from those of healthy donors (p < 0.01). Moreover, the risk score and LAG3 level of matched pairs before and after treatment samples varied significantly. Finally, an interactive nomogram consisting of the nine-gene risk group and four clinical traits was established. The inhibitors of mTOR and cyclin-dependent kinases (CDKs) were considered effective in patients in the high-risk group according to the pRRophetic algorithm. Collectively, the SE-associated nine-gene prognostic model developed here may be used to predict the prognosis and assist in the risk stratification and treatment of CLL patients in the future.
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Impact of CD39 expression on CD4+ T lymphocytes and 6q deletion on outcome of patients with chronic lymphocytic leukemia. Hematol Oncol Stem Cell Ther 2018; 12:26-31. [PMID: 30336122 DOI: 10.1016/j.hemonc.2018.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/10/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE/BACKGROUND Chronic lymphocytic leukemia is one of the commonest leukemias affecting adults. CD39 inhibits T-cell and Natural killer (NK) cell responses by hydrolyzing adenosine triphosphate and adenosine diphosphate, suppressing the immune system. We investigated expression of CD39 on CD4+ T Lymphocytes in chronic lymphocytic leukemia (CLL) patients and its relationship with deletion 6q, its association with disease stage and survival. METHODS Thirty CLL patients and 20 matched controls were included in the study. Bone marrow studies with immunophenotyping, CD39, CD38, and ZAP-70, and detection of del 6q by FISH were performed. RESULTS CD39+ CD4+ T helper cells in CLL patients were significantly expressed compared with the controls (p < .001). Levels of CD39+ CD4+ T cells were significantly expressed in high risk CLL patients. Del 6q was detected in 63.3% of patients and it correlated with CD39, CD38, and ZAP-70, and advanced stage disease. There was a significant relation between response to treatment and CD39 expression and del 6q, also there was a significant difference in overall survival (OS) between patients with and without Del 6q. CONCLUSION CD39 expression on CD4+ Tcells and del 6q act as prognostic markers in CLL. Blocking or inhibition of CD39 may be a target for new immune therapy for CLL.
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Yepes S, Torres MM, López-Kleine L. Regulatory network reconstruction reveals genes with prognostic value for chronic lymphocytic leukemia. BMC Genomics 2015; 16:1002. [PMID: 26606983 PMCID: PMC4659237 DOI: 10.1186/s12864-015-2189-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background The clinical course of chronic lymphocytic leukemia (CLL) is highly variable; some patients follow an indolent course, but others progress to a more advanced stage. The mutational status of rearranged immunoglobulin heavy chain variable (IGVH) genes in CLL is a feature that is widely recognized for dividing patients into groups that are related to their prognoses. However, the regulatory programs associated with the IGVH statuses are poorly understood, and markers that can precisely predict survival outcomes have yet to be identified. Methods In this study, (i) we reconstructed gene regulatory networks in CLL by applying an information-theoretic approach to the expression profiles of 5 cohorts. (ii) We applied master regulator analysis (MRA) to these networks to identify transcription factors (TFs) that regulate an IGVH mutational status signature. The IGVH mutational status signature was developed by searching for differentially expressed genes between the IGVH mutational statuses in numerous CLL cohorts. (iii) To evaluate the biological implication of the inferred regulators, prognostic values were determined using time to treatment (TTT) and overall survival (OS) in two different cohorts. Results A robust IGVH expression signature was obtained, and various TFs emerged as regulators of the signature in most of the reconstructed networks. The TF targets expression profiles exhibited significant differences with respect to survival, which allowed the definition of a reduced profile with a high value for OS. TCF7 and its targets stood out for their roles in progression. Conclusion TFs and their targets, which were obtained merely from inferred regulatory associations, have prognostic implications and reflect a regulatory context for prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2189-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sally Yepes
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Maria Mercedes Torres
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Liliana López-Kleine
- Departamento de Estadística, Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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Cornet E, Debliquis A, Rimelen V, Civic N, Docquier M, Troussard X, Drénou B, Matthes T. Developing Molecular Signatures for Chronic Lymphocytic Leukemia. PLoS One 2015; 10:e0128990. [PMID: 26046539 PMCID: PMC4457530 DOI: 10.1371/journal.pone.0128990] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/04/2015] [Indexed: 01/01/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a clonal malignancy of mature B cells that displays a great clinical heterogeneity, with many patients having an indolent disease that will not require intervention for many years, while others present an aggressive and symptomatic leukemia requiring immediate treatment. Although there is no cure for CLL, the disease is treatable and current standard chemotherapy regimens have been shown to prolong survival. Recent advances in our understanding of the biology of CLL have led to the identification of numerous cellular and molecular markers with potential diagnostic, prognostic and therapeutic significance. We have used the recently developed digital multiplexed gene-expression technique (DMGE) to analyze a cohort of 30 CLL patients for the presence of specific genes with known diagnostic and prognostic potential. Starting from a set of 290 genes we were able to develop a molecular signature, based on the analysis of 13 genes, which allows distinguishing CLL from normal peripheral blood and from normal B cells, and a second signature based on 24 genes, which distinguishes mutated from unmutated cases (LymphCLL Mut). A third classifier (LymphCLL Diag), based on a 44-gene signature, distinguished CLL cases from a series of other B-cell chronic lymphoproliferative disorders (n = 51). While the methodology presented here has the potential to provide a "ready to use" classification tool in routine diagnostics and clinical trials, application to larger sample numbers are still needed and should provide further insights about its robustness and utility in clinical practice.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/immunology
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Cohort Studies
- Gene Expression
- Humans
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/immunology
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Transcriptome
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Affiliation(s)
- Edouard Cornet
- CHU Caen, Laboratory of Hematology, 14000, Caen, France
- University of Caen, Medical School, 14000, Caen, France
| | - Agathe Debliquis
- Département d’Hématologie, Hôpital de Mulhouse, 68051, Mulhouse, France
| | - Valérie Rimelen
- Département d’Hématologie, Hôpital de Mulhouse, 68051, Mulhouse, France
| | - Natacha Civic
- Genomics Platform iGE3, University Medical Center, 1211, Geneva, Switzerland
| | - Mylène Docquier
- Genomics Platform iGE3, University Medical Center, 1211, Geneva, Switzerland
| | - Xavier Troussard
- CHU Caen, Laboratory of Hematology, 14000, Caen, France
- University of Caen, Medical School, 14000, Caen, France
| | - Bernard Drénou
- Département d’Hématologie, Hôpital de Mulhouse, 68051, Mulhouse, France
| | - Thomas Matthes
- Hematology Service, University Hospital Geneva, 1211, Geneva, Switzerland
- Clinical Pathology Service, University Hospital Geneva, 1211, Geneva, Switzerland
- * E-mail:
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Expression and role of RIP140/NRIP1 in chronic lymphocytic leukemia. J Hematol Oncol 2015; 8:20. [PMID: 25879677 PMCID: PMC4354752 DOI: 10.1186/s13045-015-0116-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/09/2015] [Indexed: 12/31/2022] Open
Abstract
RIP140 is a transcriptional coregulator, (also known as NRIP1), which finely tunes the activity of various transcription factors and plays very important physiological roles. Noticeably, the RIP140 gene has been implicated in the control of energy expenditure, behavior, cognition, mammary gland development and intestinal homeostasis. RIP140 is also involved in the regulation of various oncogenic signaling pathways and participates in the development and progression of solid tumors. During the past years, several papers have reported evidences linking RIP140 to hematologic malignancies. Among them, two recent studies with correlative data suggested that gene expression signatures including RIP140 can predict survival in chronic lymphocytic leukemia (CLL). This review aims to summarize the literature dealing with the expression of RIP140 in CLL and to explore the potential impact of this factor on transcription pathways which play key roles in this pathology.
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10
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Gehrke I, Bouchard ED, Beiggi S, Poeppl AG, Johnston JB, Gibson SB, Banerji V. On-Target Effect of FK866, a Nicotinamide Phosphoribosyl Transferase Inhibitor, by Apoptosis-Mediated Death in Chronic Lymphocytic Leukemia Cells. Clin Cancer Res 2014; 20:4861-72. [DOI: 10.1158/1078-0432.ccr-14-0624] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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García-Muñoz R, Llorente L. Chronic lymphocytic leukaemia: could immunological tolerance mechanisms be the origin of lymphoid neoplasms? Immunology 2014; 142:536-50. [PMID: 24645778 PMCID: PMC4107664 DOI: 10.1111/imm.12285] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/06/2014] [Accepted: 03/13/2014] [Indexed: 12/12/2022] Open
Abstract
Immunological tolerance theory in chronic lymphocytic leukaemia (CLL): we suggest that B cells that express B-cell receptors (BCR) that recognize their own BCR epitopes are viewed by immune system as 'dangerous cells'. BCR autonomous signalling may induce constant receptor editing and mistakes in allelic exclusion. The fact that whole BCR recognizes a self-antigen or foreing antigen may be irrelevant in early B cell development. In early B cells, autonomous signalling induced by recognition of the BCR's own epitopes simulates an antigen-antibody engagement. In the bone marrow this interaction is viewed as recognition of self-molecules and induces receptor editing. In mature B cells autonomous signalling by the BCR may promote 'reversible anergy' and also may correct self-reactivity induced by the somatic hypermutation mechanisms in mutated CLL B cells. However, in unmutated CLL B cells, BCR autonomous signalling in addition to self-antigen recognition augments B cell activation, proliferation and genomic instability. We suggest that CLL originates from a coordinated normal immunologic tolerance mechanism to destroy self-reactive B cells. Additional genetic damage induced by tolerance mechanisms may immortalize self-reactive B cells and transform them into a leukemia.
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Affiliation(s)
| | - Luis Llorente
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMéxico City, México
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12
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Identification of a 20-gene expression-based risk score as a predictor of clinical outcome in chronic lymphocytic leukemia patients. BIOMED RESEARCH INTERNATIONAL 2014; 2014:423174. [PMID: 24883311 PMCID: PMC4026849 DOI: 10.1155/2014/423174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 12/11/2022]
Abstract
Despite the improvement in treatment options, chronic lymphocytic leukemia (CLL) remains an incurable disease and patients show a heterogeneous clinical course requiring therapy for many of them. In the current work, we have built a 20-gene expression (GE)-based risk score predictive for patients overall survival and improving risk classification using microarray gene expression data. GE-based risk score allowed identifying a high-risk group associated with a significant shorter overall survival (OS) and time to treatment (TTT) (P ≤ .01), comprising 19.6% and 13.6% of the patients in two independent cohorts. GE-based risk score, and NRIP1 and TCF7 gene expression remained independent prognostic factors using multivariate Cox analyses and combination of GE-based risk score together with NRIP1 and TCF7 gene expression enabled the identification of three clinically distinct groups of CLL patients. Therefore, this GE-based risk score represents a powerful tool for risk stratification and outcome prediction of CLL patients and could thus be used to guide clinical and therapeutic decisions prospectively.
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Sevov M, Rosenquist R, Mansouri L. RNA-based markers as prognostic factors in chronic lymphocytic leukemia. Expert Rev Hematol 2014; 5:69-79. [DOI: 10.1586/ehm.11.80] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Rouhigharabaei L, Ferreiro JF, Put N, Michaux L, Tousseyn T, Lefebvre C, Gardiner A, De Kelver W, Demuynck H, Verschuere J, Théate I, Vicente C, Vandenberghe P, Cools J, Wlodarska I. BMI1, the polycomb-group gene, is recurrently targeted by genomic rearrangements in progressive B-cell leukemia/lymphoma. Genes Chromosomes Cancer 2013; 52:928-44. [PMID: 23873701 DOI: 10.1002/gcc.22088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/13/2013] [Indexed: 01/10/2023] Open
Abstract
BMI1, a Polycomb-group gene located at 10p12.2, is implicated in the pathogenesis of a variety of tumors. However, the genetic molecular mechanisms underlying its aberrant expression in cancer cells remain largely unknown. In this study, we show that BMI1 is recurrently targeted by chromosomal aberrations in B-cell leukemia/lymphoma. We identified a novel t(10;14)(p12;q32)/IGH-BMI1 rearrangement and its IGL variant in six cases of chronic lymphocytic leukemia (CLL) and found that these aberrations were consistently acquired at time of disease progression and high grade transformation of leukemia (Richter syndrome). The IG-BMI1 translocations were not associated with any particular molecular subtype of CLL and the leukemias were negative for common mutations of NOTCH1 and TP53, known to increase a risk of progression and transformation in CLL. In addition, using FISH and SNP array analysis, we identified a wide range of BMI1-involving 10p12 lesions in 17 cases of mantle cell lymphoma (MCL). These aberrations included various balanced and unbalanced structural abnormalities and very frequently but not exclusively, were associated with gain of the BMI1 locus and loss of the 10p terminal sequences. These findings point to genomic instability at the 10p region in MCL which likely promotes rearrangements and deregulation of BMI1. Our findings are in line with previously published observations correlating overexpression of BMI1 with tumor progression and chemoresistance. In summary, our study provides new insights into genetic molecular mechanisms underlying aberrant expression of BMI1 in lymphoma and documents its contribution in the pathogenesis of Richter syndrome and MCL.
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Rosenquist R, Cortese D, Bhoi S, Mansouri L, Gunnarsson R. Prognostic markers and their clinical applicability in chronic lymphocytic leukemia: where do we stand? Leuk Lymphoma 2013; 54:2351-64. [PMID: 23480493 DOI: 10.3109/10428194.2013.783913] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease where the majority of patients have an indolent disease course, while others may experience a far more aggressive disease, treatment failure and poor overall survival. During the last two decades, there has been an intense search to find novel biomarkers that can predict prognosis as well as guide treatment decisions. Two of the most reliable molecular prognostic markers, both of which are offered in routine diagnostics, are the immunoglobulin heavy chain variable (IGHV) gene mutational status and fluorescence in situ hybridization (FISH) detection of prognostically relevant genomic aberrations (e.g. 11q-, 13q-, +12 and 17p-). In addition to these markers, a myriad of additional biomarkers have been postulated as potential prognosticators in CLL, on the protein (e.g. CD38, ZAP70, TCL1), the RNA (e.g. LPL, CLLU1, micro-RNAs) and the genomic (e.g. TP53, NOTCH1, SF3B1 and BIRC3 mutations) level. Efforts are now being made to test these novel markers in larger patient cohorts as well as in prospective trials, with the ultimate goal to combine the "best" markers in a "CLL prognostic index" applicable for the individual patient. Although it is clear that these studies have significantly improved our knowledge regarding both prognostication and the biology of the disease, there is still an immediate need for recognizing biomarkers that can predict therapy response, and efforts should now focus on addressing this pertinent issue. In the present article, we review the extensive literature in the field of prognostic markers in CLL, focus on the most clinically relevant markers and discuss future directions regarding biomarkers in CLL.
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Affiliation(s)
- Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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16
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Hartman ML, Kilianska ZM. Lipoprotein lipase: a new prognostic factor in chronic lymphocytic leukaemia. Contemp Oncol (Pozn) 2013; 16:474-9. [PMID: 23788932 PMCID: PMC3687463 DOI: 10.5114/wo.2012.32476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 11/15/2011] [Accepted: 01/25/2012] [Indexed: 11/19/2022] Open
Abstract
The clinical course of patients with chronic lymphocytic leukemia (CLL) is highly heterogeneous. Gene expression analyses have revealed that leukemic cells with unmutated immunoglobulin heavy chain genes (IgV H ) differ from CLL cells with mutated IgV H in the expression level of some genes, i.e. encoding kinase ZAP-70 and antigen CD38. Recently, additional markers in CLL, including the expression level of apoptosis-regulating genes/proteins (Bcl-2, Mcl-1) and microRNAs, have been suggested. In this review, we attempt to provide data concerning the properties of lipoprotein lipase (LPL), as well as to present its prognostic value in CLL. LPL mRNA expression level was able to predict mutational status in a high percentage of CLL cases and high LPL expression was associated with shorter treatment-free survival. Importantly, since LPL activity is low (or absent) in other blood cell types, its expression can be determined by PCR technique in peripheral blood mononuclear cells or in lysed blood samples.
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Affiliation(s)
- Mariusz L Hartman
- Department of Medical Biochemistry, Faculty of Cytobiochemistry, University of Lodz, Poland
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Vidal L, Gafter-Gvili A, Gurion R, Raanani P, Dreyling M, Shpilberg O. Bendamustine for patients with indolent B cell lymphoid malignancies including chronic lymphocytic leukaemia. Cochrane Database Syst Rev 2012; 2012:CD009045. [PMID: 22972131 PMCID: PMC7387870 DOI: 10.1002/14651858.cd009045.pub2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Indolent B cell lymphoid malignancies include follicular lymphoma, small lymphocytic lymphoma, mantle cell lymphoma, lymphoplasmacytic lymphoma and marginal zone lymphomas. Chronic lymphocytic leukaemia (CLL) is a lymphoid malignancy similar to small lymphocytic lymphoma (SLL) in its leukaemic phase.Indolent lymphoid malignancies including CLL are characterised by slow growth, a high initial response rate and a relapsing and progressive disease course. Advanced-stage indolent B cell lymphoid malignancies are often incurable. If symptoms or progressive disease occur, chemotherapy plus rituximab is indicated. No chemotherapy regimen has been shown to improve overall survival compared to a different regimen.Bendamustine is efficacious in the treatment of patients with indolent B cell lymphoid malignancies. A number of randomised controlled trials have examined the effect of bendamustine compared to other chemotherapy regimens in these patients. Improved disease control with no survival benefit is shown. OBJECTIVES To evaluate the efficacy of bendamustine therapy for patients with indolent B cell lymphoid malignancies including CLL. SEARCH METHODS We electronically searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 2), MEDLINE (1966 to May 2012), EMBASE (1974 to November 2011), LILACS (1982 to May 2012), databases of ongoing trials (accessed 30 April 2012) and relevant conference proceedings. We searched references of identified trials and contacted the first author of each included trial. SELECTION CRITERIA Randomised controlled trials that compared a bendamustine-containing regimen to other chemotherapy with or without immunotherapy. DATA COLLECTION AND ANALYSIS Two authors independently appraised the quality of each trial and extracted data from included trials. We estimated and pooled hazard ratios (HR) and risk ratios (RR) with 95% confidence intervals (CI). MAIN RESULTS We included five trials randomising 1343 adult patients in the systematic review. Allocation and blinding were unclear in three trials and adequate in two. Incomplete outcome data and selective reporting were adequate in all trials. Trials varied in the type of lymphoid malignancy, bendamustine regimen and the comparator regimen. In the three trials that included patients with follicular lymphoma, mantle cell lymphoma and other indolent lymphomas the comparator treatment was cyclophosphamide, a combination of cyclophosphamide, vincristine, doxorubicin and prednisone, and fludarabine. Two trials included only patients with CLL and compared bendamustine to chlorambucil, and to fludarabine. We did not conduct a meta-analysis due to the clinical heterogeneity among trials. Bendamustine had no statistically significant effect on the overall survival of patients with indolent B cell lymphoid malignancies in any of the included trials (trials of moderate quality). Progression-free survival was statistically significantly improved with bendamustine treatment compared to other chemotherapy in three of the four trials that reported on it. One trial demonstrated a non statistically significant improvement of PFS. The risk of grade 3 or 4 adverse events was similar when bendamustine was compared to CHOP and fludarabine, and higher when compared to chlorambucil. Compared to chlorambucil quality of life was unaffected by bendamustine treatment (one trial, no meta-analysis). AUTHORS' CONCLUSIONS As none of the currently available chemotherapeutic protocols for induction therapy in indolent B cell lymphoid malignancies confer a survival benefit and due to the improved progression-free survival in each of the included trials, and a similar rate of grade 3 or 4 adverse events, bendamustine may be considered for the treatment of patients with indolent B cell lymphoid malignancies. However, the unclear effect on survival and the higher rate of adverse events compared to chlorambucil in patients with CLL/SLL does not support the use of bendamustine for these patients.The effect of bendamustine combined with rituximab should be evaluated in randomised clinical trials with more homogenous populations and outcomes for specific subgroups of patients by type of lymphoma should be reported. Any future trial should evaluate the effect of bendamustine on quality of life.
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MESH Headings
- Adult
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Bendamustine Hydrochloride
- Cyclophosphamide/administration & dosage
- Cyclophosphamide/therapeutic use
- Doxorubicin/administration & dosage
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Lymphoma, B-Cell/drug therapy
- Lymphoma, B-Cell/mortality
- Lymphoma, Follicular/drug therapy
- Lymphoma, Follicular/mortality
- Lymphoma, Mantle-Cell/drug therapy
- Lymphoma, Mantle-Cell/mortality
- Nitrogen Mustard Compounds/therapeutic use
- Prednisone/administration & dosage
- Recurrence
- Vincristine/administration & dosage
- Waldenstrom Macroglobulinemia/drug therapy
- Waldenstrom Macroglobulinemia/mortality
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Affiliation(s)
- Liat Vidal
- Department of Medicine E, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel.
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Vidal L, Gurion R, Gafter-Gvili A, Raanani P, Robak T, Shpilberg O. Chlorambucil for the treatment of patients with chronic lymphocytic leukaemia, or small lymphocytic lymphoma. Hippokratia 2011. [DOI: 10.1002/14651858.cd009341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Liat Vidal
- Beilinson Hospital, Rabin Medical Center; Department of Medicine E; 39 Jabotinski Street Petah Tikva Israel 49100
| | - Ronit Gurion
- Beilinson Hospital, Rabin Medical Center; Institute of Hematology, Davidoff Center; 39 Jabotinski Street Petah Tikva Israel 49100
| | - Anat Gafter-Gvili
- Beilinson Hospital, Rabin Medical Center; Department of Medicine E; 39 Jabotinski Street Petah Tikva Israel 49100
| | - Pia Raanani
- Beilinson Hospital, Rabin Medical Center; Institute of Hematology, Davidoff Center; 39 Jabotinski Street Petah Tikva Israel 49100
| | - Tadeusz Robak
- Medical University of Lodz and Copernicus Memorial Hospital; Department of Hematology; Lodz Poland
| | - Ofer Shpilberg
- Beilinson Hospital, Rabin Medical Center; Institute of Hematology, Davidoff Center; 39 Jabotinski Street Petah Tikva Israel 49100
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Rampazzo E, Bonaldi L, Trentin L, Visco C, Keppel S, Giunco S, Frezzato F, Facco M, Novella E, Giaretta I, Del Bianco P, Semenzato G, De Rossi A. Telomere length and telomerase levels delineate subgroups of B-cell chronic lymphocytic leukemia with different biological characteristics and clinical outcomes. Haematologica 2011; 97:56-63. [PMID: 21933855 DOI: 10.3324/haematol.2011.049874] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND B-cell chronic lymphocytic leukemia is a clinically heterogeneous disease; some patients rapidly progress and die within a few years of diagnosis, whereas others have a long life expectancy with minimal or no treatment. Telomere length and telomerase levels have been proposed as prognostic factors; however, very few cases have been characterized for both parameters and no study has analyzed the prognostic value of the telomere/telomerase profile. DESIGN AND METHODS One hundred and seventy-three cases of chronic lymphocytic leukemia were characterized for telomere lengths and telomerase levels by real-time polymerase chain reaction. Data were correlated with established prognostic markers, IGVH mutational status and chromosomal aberrations, and clinical outcome. RESULTS Telomere lengths were inversely correlated with telomerase levels (r(s) = -0.213; P = 0.012), and most of the cases of chronic lymphocytic leukemia with high levels (above median) of telomerase had short (below median) telomeres (P = 0.0001). Telomerase levels were higher and telomeres were shorter in unmutated IGVH cases than in mutated IGVH ones (P<0.0001). Chronic lymphocytic leukemias with 11q, 17p deletion or 12 trisomy had significantly higher levels of telomerase and shorter telomeres than those with no chromosomal aberration or the sole 13q deletion (P < 0.001). Telomere length/telomerase level profiles identified subgroups of patients with different clinical outcomes (P < 0.0001), even within the subsets of chronic lymphocytic leukemia defined by IGVH mutational status or chromosomal aberrations. Short telomere/high telomerase profile was independently associated with more rapid disease progression. CONCLUSIONS Comprehensive analyses of telomeres, telomerase, chromosomal aberrations, and IGVH mutational status delineate groups of chronic lymphocytic leukemias with distinct biological characteristics and clinical outcomes. The telomere/telomerase profile may be particularly useful in refining the prognosis of chronic lymphocytic leukemia patients with mutated IGVH and no high-risk chromosomal aberrations.
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Affiliation(s)
- Enrica Rampazzo
- Department of Oncology and Surgical Sciences, Oncology Section, University of Padova,Padova, Italy
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Moreno C, Montserrat E. Genetic lesions in chronic lymphocytic leukemia: what's ready for prime time use? Haematologica 2011; 95:12-5. [PMID: 20065079 DOI: 10.3324/haematol.2009.016873] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Kaderi MA, Kanduri M, Buhl AM, Sevov M, Cahill N, Gunnarsson R, Jansson M, Smedby KE, Hjalgrim H, Jurlander J, Juliusson G, Mansouri L, Rosenquist R. LPL is the strongest prognostic factor in a comparative analysis of RNA-based markers in early chronic lymphocytic leukemia. Haematologica 2011; 96:1153-60. [PMID: 21508119 PMCID: PMC3148909 DOI: 10.3324/haematol.2010.039396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The expression levels of LPL, ZAP70, TCL1A, CLLU1 and MCL1 have recently been proposed as prognostic factors in chronic lymphocytic leukemia. However, few studies have systematically compared these different RNA-based markers. DESIGN AND METHODS Using real-time quantitative PCR, we measured the mRNA expression levels of these genes in unsorted samples from 252 newly diagnosed chronic lymphocytic leukemia patients and correlated our data with established prognostic markers (for example Binet stage, CD38, IGHV gene mutational status and genomic aberrations) and clinical outcome. RESULTS High expression levels of all RNA-based markers, except MCL1, predicted shorter overall survival and time to treatment, with LPL being the most significant. In multivariate analysis including the RNA-based markers, LPL expression was the only independent prognostic marker for overall survival and time to treatment. When studying LPL expression and the established markers, LPL expression retained its independent prognostic strength for overall survival. All of the RNA-based markers, albeit with varying ability, added prognostic information to established markers, with LPL expression giving the most significant results. Notably, high LPL expression predicted a worse outcome in good-prognosis subgroups, such as patients with mutated IGHV genes, Binet stage A, CD38 negativity or favorable cytogenetics. In particular, the combination of LPL expression and CD38 could further stratify Binet stage A patients. CONCLUSIONS LPL expression is the strongest RNA-based prognostic marker in chronic lymphocytic leukemia that could potentially be applied to predict outcome in the clinical setting, particularly in the large group of patients with favorable prognosis.
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MESH Headings
- Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Female
- Humans
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lipoprotein Lipase/genetics
- Lipoprotein Lipase/metabolism
- Male
- Middle Aged
- Multivariate Analysis
- Mutation/genetics
- Prognosis
- RNA, Messenger/metabolism
- Survival Analysis
- Treatment Outcome
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Affiliation(s)
- Mohd Arifin Kaderi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Basic Health Sciences, KAHS IIUM Kuantan Campus, Pahang, Malaysia
| | - Meena Kanduri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anne Mette Buhl
- Department of Hematology, Leukemia Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Marie Sevov
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Nicola Cahill
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rebeqa Gunnarsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Mattias Jansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Karin Ekström Smedby
- Department of Medicine, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Jurlander
- Department of Hematology, Leukemia Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Herold T, Jurinovic V, Metzeler KH, Boulesteix AL, Bergmann M, Seiler T, Mulaw M, Thoene S, Dufour A, Pasalic Z, Schmidberger M, Schmidt M, Schneider S, Kakadia PM, Feuring-Buske M, Braess J, Spiekermann K, Mansmann U, Hiddemann W, Buske C, Bohlander SK. An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia. Leukemia 2011; 25:1639-45. [PMID: 21625232 DOI: 10.1038/leu.2011.125] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Zenz T, Fröhling S, Mertens D, Döhner H, Stilgenbauer S. Moving from prognostic to predictive factors in chronic lymphocytic leukaemia (CLL). Best Pract Res Clin Haematol 2011; 23:71-84. [PMID: 20620972 DOI: 10.1016/j.beha.2009.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many prognostic factors have been identified in chronic lymphocytic leukaemia (CLL). Based on the assessment of B cell receptor (BCR) structure and function, a subdivision into subtypes is possible (e.g., immunoglobulin heavy chain variable gene segment (IGHV) unmutated and mutated, V3-21 usage) with distinct biological and clinical characteristics. Recurrent genomic aberrations (i.e., 11q and 17p deletion) and gene mutations (i.e., TP53 and ATM) help to define biological and clinical subgroups. In addition, serum markers (e.g., thymidine kinase (TK) and beta2-microglobulin (beta2-MG)), cellular markers (e.g., CD38 and ZAP70) and clinical staging have an impact on outcome in CLL. The biological characterisation of CLL has not only led to progress in outcome prediction but also has begun to be translated into novel treatment strategies. Nonetheless, most factors associated with prognosis have not been thoroughly interrogated for their predictive value in the light of different therapeutic approaches. With a growing number of agents acting on specific biological targets and being used in different clinical situations, the future is likely to bring the identification of predictive factors in CLL.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Predictive Value of Tests
- Prognosis
- Receptors, Antigen, B-Cell/immunology
- Risk Factors
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Affiliation(s)
- Thorsten Zenz
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
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Stamatopoulos B, Meuleman N, De Bruyn C, Pieters K, Anthoine G, Mineur P, Bron D, Lagneaux L. A molecular score by quantitative PCR as a new prognostic tool at diagnosis for chronic lymphocytic leukemia patients. PLoS One 2010; 5:e12780. [PMID: 20862275 PMCID: PMC2940823 DOI: 10.1371/journal.pone.0012780] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 08/22/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Several markers have been proposed to predict the outcome of chronic lymphocytic leukemia (CLL) patients. However, discordances exist between the current prognostic factors, indicating that none of these factors are totally perfect. METHODOLOGY/PRINCIPAL FINDINGS Here, we compared the prognostic power of new RNA-based markers in order to construct a quantitative PCR (qPCR) score composed of the most powerful factors. ZAP70, LPL, CLLU1, microRNA-29c and microRNA-223 were measured by real time PCR in a cohort of 170 patients with a median follow-up of 64 months (range3-330). For each patient, cells were obtained at diagnosis and RNA was extracted from purified CD19 cells. The best markers were included in a qPCR score, which was thereafter compared to each individual factor. Statistical analysis showed that all five RNA-based markers can predict treatment-free survival (TFS), but only ZAP70, LPL and microRNA-29c could significantly predict overall survival (OS). These three markers were thus included in a simple qPCR score that was able to significantly predict TFS and OS by dividing patients into three groups (0/3, 1-2/3 and 3/3). Median TFS were >210, 61 and 24 months (P<0.0001) and median OS were >330, 242 and 137 months (P<0.0001), respectively. Interestingly, TFS results were also confirmed in Binet stage A patients (P<0.0001). When compared to other classical factors, this score displays the highest univariate Cox hazard ratio (TFS: HR=9.45 and OS: HR=13.88) but also provides additional prognostic information. CONCLUSIONS In our hands, this score is the most powerful tool for CLL risk stratification at the time of diagnosis.
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Affiliation(s)
- Basile Stamatopoulos
- Laboratory of Experimental Hematology, Faculty of Medicine, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
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Abstract
An increasing number of neoplasms are associated with variably specific genetic abnormalities. This is best exemplified by hematological malignancies, in which there is a growing list of entities that are defined by their genetic lesion(s); this is not (yet) the case in mature B-cell lymphomas. However, enhanced insights into the pathogenesis of this large and diverse group of lymphomas have emerged with the ongoing unraveling of a plethora of fascinating genetic abnormalities. The purpose of this review is to synthesize well-recognized data and nascent discoveries in our understanding of the genetic basis of a spectrum of mature B-cell lymphomas, and how this may be applied to contemporary clinical practice. Despite the explosion of new and exciting knowledge in this arena, with the potential for enhanced diagnostic and prognostic strategies, it is essential to remain cognizant of the limitations (and complexity) of genetic investigations, so that assays can be developed and used both judiciously and rationally.
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Valceckiene V, Kontenyte R, Jakubauskas A, Griskevicius L. Selection of reference genes for quantitative polymerase chain reaction studies in purified B cells from B cell chronic lymphocytic leukaemia patients. Br J Haematol 2010; 151:232-8. [DOI: 10.1111/j.1365-2141.2010.08363.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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